[adegenet-commits] r884 - in pkg: R inst/doc inst/doc/figs
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri May 27 18:45:15 CEST 2011
Author: jombart
Date: 2011-05-27 18:45:15 +0200 (Fri, 27 May 2011)
New Revision: 884
Modified:
pkg/R/dapc.R
pkg/inst/doc/adegenet-dapc.Rnw
pkg/inst/doc/figs/-006.pdf
pkg/inst/doc/figs/-010.pdf
pkg/inst/doc/figs/-011.pdf
pkg/inst/doc/figs/-012.pdf
pkg/inst/doc/figs/-013.pdf
pkg/inst/doc/figs/-015.pdf
pkg/inst/doc/figs/-016.pdf
pkg/inst/doc/figs/-019.pdf
pkg/inst/doc/figs/-020.pdf
pkg/inst/doc/figs/-021.pdf
pkg/inst/doc/figs/-022.pdf
pkg/inst/doc/figs/-024.pdf
pkg/inst/doc/figs/-026.pdf
pkg/inst/doc/figs/-028.pdf
pkg/inst/doc/figs/-033.pdf
pkg/inst/doc/figs/-034.pdf
Log:
Tutorial not finished; need to fix threshold in loadingplot.
Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/R/dapc.R 2011-05-27 16:45:15 UTC (rev 884)
@@ -878,6 +878,7 @@
## centre/scale data
for(i in 1:nrow(newdata)){ # this is faster for large, flat matrices)
newdata[i,] <- (newdata[i,] - object$pca.cent) / object$pca.norm
+ newdata[i, is.na(newdata[i, ])] <- 0 # replace NAs
}
## project as supplementary individuals
Modified: pkg/inst/doc/adegenet-dapc.Rnw
===================================================================
--- pkg/inst/doc/adegenet-dapc.Rnw 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/adegenet-dapc.Rnw 2011-05-27 16:45:15 UTC (rev 884)
@@ -421,10 +421,35 @@
\subsection{Interpreting variable contributions}
%%%%%%%%%%%%%%%%
+In DAPC, the variable actually analyzed are principal components of a PCA.
+Loadings of these variables are generally uninformative.
+However, we also compute contributions of the alleles, which can be interpreted and sometimes very informative.
+In general, there are many alleles and their contribution is best plotted for a single discriminant
+function at a time.
+Variable contributions are stored in the \texttt{var.contr} slot of a \texttt{dapc} object.
+They can be plotted using \texttt{loadingplot}.
+We illustrate this using the seasonal influenza dataset \texttt{H3N2}:
+<<>>=
+data(H3N2)
+H3N2
+dapc.flu <- dapc(H3N2, pop=H3N2$other$epid, n.pca=30,n.da=10)
+@
+The first discriminant function shows the temporal evolution of the influenza virus, while the
+second one shows the originality of 2006 strains.
+<<fig=TRUE>>=
+scatter(dapc.flu, col=transp(myPal(6)), ratio=0, cell=0, cex=2, bg="white",cstar=0)
+@
+We can assess which alleles most highlight the originality of 2006 using \texttt{loadingplot}:
+<<fig=TRUE>>=
+temp <- loadingplot(dapc.flu$var.contr, thres=.5)
+@
+
+
+
%%%%%%%%%%%%%%%%
\subsection{Interpreting group memberships}
%%%%%%%%%%%%%%%%
@@ -621,12 +646,12 @@
<<fig=TRUE>>=
temp <- which(apply(dapc3$posterior,1, function(e) all(e<0.5)))
temp
-lab <- pop(microbov)[temp]
+lab <- pop(microbov)
par(mar=c(8,4,5,1), xpd=TRUE)
-compoplot(dapc3, subset=temp, cleg=.6, posi=list(x=0,y=1.2))
+compoplot(dapc3, subset=temp, cleg=.6, posi=list(x=0,y=1.2),lab=lab)
@
-\noindent Admixture seems strongest between a few breeds (Blonde d'Aquitaine, Bretonne Pie-Noire,
+\noindent Admixture appears to be the strongest between a few breeds (Blonde d'Aquitaine, Bretonne Pie-Noire,
Limousine and Gascone). Some features are fairly surprising; for instance, the last individual is
fairly distant from its cluster, but almost 50\% chances to be assigned to two other breeds.
@@ -641,21 +666,72 @@
%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%
-
-
%%%%%%%%%%%%%%%%
\subsection{Rationale}
%%%%%%%%%%%%%%%%
+Statistically speaking, supplementary individuals are observations which did not participate to the
+analysis, but which we would like to predict using our model of the data.
+In the context of DAPC, we may know groups for most individuals, but some individuals could be of
+unknown or uncertain group. In this case, we need to exclude individuals from the analysis, and then
+project them as supplementary individuals on the discriminant functions.
+The only requirement for this operation is that supplementary individuals have been typed as the
+same loci as the rest of the dataset.
-%%%%%%%%%%%%%%%%
-\subsection{Predicting group membership}
-%%%%%%%%%%%%%%%%
+Technically, using supplementary individuals consist in transforming the new data using the centring
+and scaling of the contributing individuals, and then using the same discriminant coefficients as
+for the contributing individuals to predict the position of the new individuals onto the
+discriminant functions.
%%%%%%%%%%%%%%%%
-\subsection{Representing supplementary individuals}
+\subsection{In practice}
%%%%%%%%%%%%%%%%
+We will illustrate the practice of supplementary individuals using the cattle breeds data previously
+analyzed (\texttt{microbov} dataset).
+We first split the dataset into two parts: one used for the analysis, and one used as supplementary individuals:
+<<>>=
+data(microbov)
+kept.id <- unlist(tapply(1:nInd(microbov), pop(microbov), function(e) sample(e, 30,replace=FALSE)))
+x <- microbov[kept.id]
+x.sup <- microbov[-kept.id]
+nInd(x)
+nInd(x.sup)
+@
+\texttt{x} is a \texttt{genind} containing the data to be analyzed; \texttt{x.sup} contains the
+supplementary individuals.
+We perform the DAPC of \texttt{x}, and use \texttt{predict} to predict results for the
+supplementary individuals:
+<<>>=
+dapc4 <- dapc(x,n.pca=20,n.da=15)
+pred.sup <- predict.dapc(dapc4, newdata=x.sup)
+names(pred.sup)
+head(pred.sup$assign)
+pred.sup$ind.scores[1:5,1:3]
+round(pred.sup$posterior[1:5, 1:5],3)
+@
+
+\noindent The list \texttt{pred.sup} contains all the predictions about the new data based on the
+analysis stored in \texttt{dapc4}. The slot \texttt{assign} contains the assignment of new individuals
+to groups; \texttt{ind.scores} contains the coordinates of the new individuals on the discriminant
+functions; \texttt{posterior} contains the posterior membership probabilities.
+We can visualize the information by different ways.
+First, we can represent the new individuals using a scatterplot, and see :
+<<fig=TRUE>>=
+col <- rainbow(length(levels(pop(x))))
+col.points <- transp(col[as.integer(pop(x))],.1)
+scatter(dapc4, col=col, bg="white", ratio=0, grid=FALSE, pch="", cstar=0, axesel=FALSE, clab=0, lwd=3, xlim=c(-10,10))
+par(xpd=TRUE)
+points(dapc4$ind.coord[,1], dapc4$ind.coord[,2], pch=20, col=col.points, cex=5)
+col.sup <- col[as.integer(pop(x.sup))]
+points(pred.sup$ind.scores[,1], pred.sup$ind.scores[,2], pch=15, col=transp(col.sup,.7), cex=2)
+legend("bottomright", fill=col, leg=levels(pop(x)), ncol=2, cex=.7, bg=transp("white"))
+add.scatter.eig(dapc4$eig,15,1,2, posi="topright", inset=.02)
+@
+
+\noindent Light dots and ellipses correspond to the original analysis, while more solid squares indicate
+supplementary individuals.
+
\end{document}
Modified: pkg/inst/doc/figs/-006.pdf
===================================================================
--- pkg/inst/doc/figs/-006.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-006.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152608)
-/ModDate (D:20110527152608)
+/CreationDate (D:20110527165917)
+/ModDate (D:20110527165917)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-010.pdf
===================================================================
--- pkg/inst/doc/figs/-010.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-010.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152609)
-/ModDate (D:20110527152609)
+/CreationDate (D:20110527165917)
+/ModDate (D:20110527165917)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-011.pdf
===================================================================
--- pkg/inst/doc/figs/-011.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-011.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152609)
-/ModDate (D:20110527152609)
+/CreationDate (D:20110527165917)
+/ModDate (D:20110527165917)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-012.pdf
===================================================================
--- pkg/inst/doc/figs/-012.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-012.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152609)
-/ModDate (D:20110527152609)
+/CreationDate (D:20110527165917)
+/ModDate (D:20110527165917)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-013.pdf
===================================================================
--- pkg/inst/doc/figs/-013.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-013.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152609)
-/ModDate (D:20110527152609)
+/CreationDate (D:20110527165918)
+/ModDate (D:20110527165918)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-015.pdf
===================================================================
--- pkg/inst/doc/figs/-015.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-015.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152610)
-/ModDate (D:20110527152610)
+/CreationDate (D:20110527165918)
+/ModDate (D:20110527165918)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-016.pdf
===================================================================
--- pkg/inst/doc/figs/-016.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-016.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152610)
-/ModDate (D:20110527152610)
+/CreationDate (D:20110527165918)
+/ModDate (D:20110527165918)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-019.pdf
===================================================================
--- pkg/inst/doc/figs/-019.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-019.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152610)
-/ModDate (D:20110527152610)
+/CreationDate (D:20110527165918)
+/ModDate (D:20110527165918)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-020.pdf
===================================================================
--- pkg/inst/doc/figs/-020.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-020.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152610)
-/ModDate (D:20110527152610)
+/CreationDate (D:20110527165918)
+/ModDate (D:20110527165918)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-021.pdf
===================================================================
--- pkg/inst/doc/figs/-021.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-021.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152610)
-/ModDate (D:20110527152610)
+/CreationDate (D:20110527165919)
+/ModDate (D:20110527165919)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-022.pdf
===================================================================
--- pkg/inst/doc/figs/-022.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-022.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152610)
-/ModDate (D:20110527152610)
+/CreationDate (D:20110527165919)
+/ModDate (D:20110527165919)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-024.pdf
===================================================================
--- pkg/inst/doc/figs/-024.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-024.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152612)
-/ModDate (D:20110527152612)
+/CreationDate (D:20110527165920)
+/ModDate (D:20110527165920)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-026.pdf
===================================================================
--- pkg/inst/doc/figs/-026.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-026.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152615)
-/ModDate (D:20110527152615)
+/CreationDate (D:20110527165924)
+/ModDate (D:20110527165924)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-028.pdf
===================================================================
--- pkg/inst/doc/figs/-028.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-028.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152618)
-/ModDate (D:20110527152618)
+/CreationDate (D:20110527165927)
+/ModDate (D:20110527165927)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
@@ -37,67 +37,67 @@
1 J
1 j
10.00 M
-111.07 77.87 282.45 18.35 re B
-111.07 99.89 295.59 18.35 re B
-111.07 121.91 280.66 18.35 re B
-111.07 143.93 281.51 18.35 re B
-111.07 165.96 295.59 18.35 re B
-111.07 187.98 262.74 18.35 re B
-111.07 210.00 251.15 18.35 re B
-111.07 232.02 296.13 18.35 re B
-111.07 254.05 295.59 18.35 re B
-111.07 276.07 289.02 18.35 re B
-111.07 298.09 306.53 18.35 re B
-111.07 320.11 296.65 18.35 re B
-111.07 342.14 265.54 18.35 re B
-111.07 364.16 289.02 18.35 re B
-111.07 386.18 269.31 18.35 re B
+111.07 77.87 286.02 18.35 re B
+111.07 99.89 244.33 18.35 re B
+111.07 121.91 247.34 18.35 re B
+111.07 143.93 279.05 18.35 re B
+111.07 165.96 260.03 18.35 re B
+111.07 187.98 276.75 18.35 re B
+111.07 210.00 266.37 18.35 re B
+111.07 232.02 306.53 18.35 re B
+111.07 254.05 304.42 18.35 re B
+111.07 276.07 283.37 18.35 re B
+111.07 298.09 271.80 18.35 re B
+111.07 320.11 266.37 18.35 re B
+111.07 342.14 279.05 18.35 re B
+111.07 364.16 295.96 18.35 re B
+111.07 386.18 286.42 18.35 re B
Q q
BT
/sRGB cs 0.000 0.000 0.000 scn
-/F2 1 Tf 12.00 0.00 -0.00 12.00 54.91 82.73 Tm (Borgou) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 40.24 82.73 Tm (Lagunaire) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 56.06 104.76 Tm [(A) 30 (ubr) 10 (ac)] TJ
+/F2 1 Tf 12.00 0.00 -0.00 12.00 6.22 104.76 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 42.92 126.78 Tm (Charolais) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 45.59 126.78 Tm (Limousin) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 30.24 148.80 Tm (MaineAnjou) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 55.58 148.80 Tm (Somba) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 52.93 170.82 Tm (NDama) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 56.06 170.82 Tm [(A) 30 (ubr) 10 (ac)] TJ
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 52.25 192.85 Tm (Gascon) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 42.92 192.85 Tm (Charolais) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 40.24 214.87 Tm (Lagunaire) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 52.25 214.87 Tm (Gascon) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 6.22 236.89 Tm (BlondeAquitaine) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 30.91 236.89 Tm (Montbeliard) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 66.49 258.91 Tm [(Zeb) 20 (u)] TJ
+/F2 1 Tf 12.00 0.00 -0.00 12.00 54.91 258.91 Tm (Borgou) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 45.59 280.94 Tm (Limousin) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 44.24 280.94 Tm (Bazadais) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 30.91 302.96 Tm (Montbeliard) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 30.24 302.96 Tm (MaineAnjou) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 25.58 324.98 Tm (BretPieNoire) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 59.59 324.98 Tm (Salers) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 44.24 347.00 Tm (Bazadais) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 66.49 347.00 Tm [(Zeb) 20 (u)] TJ
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 59.59 369.03 Tm (Salers) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 52.93 369.03 Tm (NDama) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 55.58 391.05 Tm (Somba) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 25.58 391.05 Tm (BretPieNoire) Tj
ET
Q q
BT
@@ -111,27 +111,27 @@
1 J
1 j
10.00 M
-111.07 64.80 m 373.81 64.80 l S
+111.07 64.80 m 364.75 64.80 l S
111.07 64.80 m 111.07 57.60 l S
-176.75 64.80 m 176.75 57.60 l S
-242.44 64.80 m 242.44 57.60 l S
-308.12 64.80 m 308.12 57.60 l S
-373.81 64.80 m 373.81 57.60 l S
+174.49 64.80 m 174.49 57.60 l S
+237.91 64.80 m 237.91 57.60 l S
+301.33 64.80 m 301.33 57.60 l S
+364.75 64.80 m 364.75 57.60 l S
BT
/sRGB cs 0.000 0.000 0.000 scn
/F2 1 Tf 12.00 0.00 -0.00 12.00 107.73 38.88 Tm (0) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 170.08 38.88 Tm (20) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 167.81 38.88 Tm (20) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 235.77 38.88 Tm (40) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 231.24 38.88 Tm (40) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 301.45 38.88 Tm (60) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 294.66 38.88 Tm (60) Tj
ET
BT
-/F2 1 Tf 12.00 0.00 -0.00 12.00 367.14 38.88 Tm (80) Tj
+/F2 1 Tf 12.00 0.00 -0.00 12.00 358.08 38.88 Tm (80) Tj
ET
Q
endstream
Modified: pkg/inst/doc/figs/-033.pdf
===================================================================
--- pkg/inst/doc/figs/-033.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-033.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152623)
-/ModDate (D:20110527152623)
+/CreationDate (D:20110527165932)
+/ModDate (D:20110527165932)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
Modified: pkg/inst/doc/figs/-034.pdf
===================================================================
--- pkg/inst/doc/figs/-034.pdf 2011-05-27 13:27:31 UTC (rev 883)
+++ pkg/inst/doc/figs/-034.pdf 2011-05-27 16:45:15 UTC (rev 884)
@@ -2,8 +2,8 @@
%âãÏÓ\r
1 0 obj
<<
-/CreationDate (D:20110527152623)
-/ModDate (D:20110527152623)
+/CreationDate (D:20110527165932)
+/ModDate (D:20110527165932)
/Title (R Graphics Output)
/Producer (R 2.13.0)
/Creator (R)
@@ -933,94 +933,94 @@
Q q
BT
/sRGB cs 0.000 0.000 0.000 scn
-/F2 1 Tf 0.00 12.00 -12.00 0.00 79.90 21.43 Tm (AFBIBOR9511) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 79.90 62.11 Tm (Borgou) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 91.07 20.15 Tm [(FRBT) 120 (A) 50 (UB9062)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 91.07 63.26 Tm [(A) 30 (ubr) 10 (ac)] TJ
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 102.24 20.15 Tm [(FRBT) 120 (A) 50 (UB9070)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 102.24 63.26 Tm [(A) 30 (ubr) 10 (ac)] TJ
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 113.42 20.15 Tm [(FRBT) 120 (A) 50 (UB9078)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 113.42 63.26 Tm [(A) 30 (ubr) 10 (ac)] TJ
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 124.59 20.15 Tm [(FRBT) 120 (A) 50 (UB9225)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 124.59 63.26 Tm [(A) 30 (ubr) 10 (ac)] TJ
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 135.76 11.92 Tm [(FRBTBD) 40 (A29851)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 135.76 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 146.94 11.92 Tm [(FRBTBD) 40 (A29856)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 146.94 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 158.11 11.92 Tm [(FRBTBD) 40 (A29879)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 158.11 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 169.28 11.92 Tm [(FRBTBD) 40 (A35248)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 169.28 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 180.46 11.92 Tm [(FRBTBD) 40 (A35256)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 180.46 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 191.63 11.92 Tm [(FRBTBD) 40 (A35259)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 191.63 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 202.80 11.92 Tm [(FRBTBD) 40 (A35267)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 202.80 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 213.98 11.92 Tm [(FRBTBD) 40 (A35278)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 213.98 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 225.15 11.92 Tm [(FRBTBD) 40 (A35281)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 225.15 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 236.32 11.92 Tm [(FRBTBD) 40 (A35877)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 236.32 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 247.49 11.92 Tm [(FRBTBD) 40 (A35941)] TJ
+/F2 1 Tf 0.00 12.00 -12.00 0.00 247.49 13.42 Tm (BlondeAquitaine) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 258.67 18.11 Tm (FRBTBPN1906) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 258.67 32.78 Tm (BretPieNoire) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 269.84 18.11 Tm (FRBTBPN1913) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 269.84 32.78 Tm (BretPieNoire) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 281.01 18.11 Tm (FRBTBPN1915) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 281.01 32.78 Tm (BretPieNoire) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 292.19 10.78 Tm (FRBTCHA15957) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 292.19 50.12 Tm (Charolais) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 303.36 10.76 Tm (FRBTGAS14183) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 303.36 59.45 Tm (Gascon) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 314.53 17.44 Tm (FRBTGAS9173) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 314.53 59.45 Tm (Gascon) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 325.71 17.44 Tm (FRBTGAS9200) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 325.71 59.45 Tm (Gascon) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 336.88 16.10 Tm (FRBTLIM30832) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 336.88 52.79 Tm (Limousin) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 348.05 16.10 Tm (FRBTLIM30839) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 348.05 52.79 Tm (Limousin) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 359.23 16.10 Tm (FRBTLIM30855) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 359.23 52.79 Tm (Limousin) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 370.40 18.11 Tm (FRBTMA25298) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 370.40 37.44 Tm (MaineAnjou) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 381.57 16.78 Tm (FRBTMBE1496) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 381.57 38.11 Tm (Montbeliard) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 392.75 16.78 Tm (FRBTMBE1514) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 392.75 38.11 Tm (Montbeliard) Tj
ET
BT
-/F2 1 Tf 0.00 12.00 -12.00 0.00 403.92 16.78 Tm (FRBTMBE1544) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 403.92 38.11 Tm (Montbeliard) Tj
ET
Q q
BT
@@ -1167,7 +1167,7 @@
endstream
endobj
9 0 obj
-32513
+32400
endobj
3 0 obj
<<
@@ -1430,18 +1430,18 @@
0000000000 65535 f
0000000021 00000 n
0000000164 00000 n
-0000032880 00000 n
-0000032963 00000 n
-0000033115 00000 n
-0000033148 00000 n
+0000032767 00000 n
+0000032850 00000 n
+0000033002 00000 n
+0000033035 00000 n
0000000213 00000 n
0000000293 00000 n
-0000032859 00000 n
-0000042684 00000 n
-0000042942 00000 n
-0000043040 00000 n
-0000043089 00000 n
-0000043138 00000 n
+0000032746 00000 n
+0000042571 00000 n
+0000042829 00000 n
+0000042927 00000 n
+0000042976 00000 n
+0000043025 00000 n
trailer
<<
/Size 15
@@ -1449,5 +1449,5 @@
/Root 2 0 R
>>
startxref
-43187
+43074
%%EOF
More information about the adegenet-commits
mailing list